Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3′ untranslated regions (3′ UTRs) of mRNAs

BMC Bioinformatics

Chris M Brown²  Ambarish Biswas¹ 

[1]Department of Biochemistry, Genetics Otago, University of Otago, Dunedin, New Zealand

[2]Genetics Otago, University of Otago, Dunedin, New Zealand

关键词: Translational control;    RNA binding protein;    microRNA;    Untranslated region;   

Others  :  818464
DOI  :  10.1186/1471-2105-15-174

 received in 2014-02-10, accepted in 2014-05-16,  发布年份 2014

【 摘 要 】

Background

Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly the 3′UTRs.

Results

Scan for Motifs (SFM) simplifies the process of identifying a wide range of regulatory elements on alignments of vertebrate 3′UTRs. SFM includes identification of both RNA Binding Protein (RBP) sites and targets of miRNAs. In addition to searching pre-computed alignments, the tool provides users the flexibility to search their own sequences or alignments. The regulatory elements may be filtered by expected value cutoffs and are cross-referenced back to their respective sources and literature. The output is an interactive graphical representation, highlighting potential regulatory elements and overlaps between them. The output also provides simple statistics and links to related resources for complementary analyses. The overall process is intuitive and fast. As SFM is a free web-application, the user does not need to install any software or databases.

Conclusions

Visualisation of the binding sites of different classes of effectors that bind to 3′UTRs will facilitate the study of regulatory elements in 3′ UTRs.

【 授权许可】

   
2014 Biswas and Brown; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

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